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% function [varargout] = spec_read(specDatFile, varargin)
% call 'spec_read()' for further help
%
% please reports bugs, problems, suggestions for improvements to:
% CXS group
%
% the case of duplicate scannumbers in the spec file, and how to
% address them remains to be implemented
%*-----------------------------------------------------------------------*
%|                                                                       |
%|  Except where otherwise noted, this work is licensed under a          |
%|  Creative Commons Attribution-NonCommercial-ShareAlike 4.0            |
%|  International (CC BY-NC-SA 4.0) license.                             |
%|                                                                       |
%|  Copyright (c) 2017 by Paul Scherrer Institute (http://www.psi.ch)    |
%|                                                                       |
%|      Author: CXS group, PSI  |
%*-----------------------------------------------------------------------*
% You may use this code with the following provisions:
%
% If the code is fully or partially redistributed, or rewritten in another
% computing language this notice should be included in the redistribution.
%
% If this code, or subfunctions or parts of it, is used for research in a
% publication or if it is fully or partially rewritten for another
% computing language the authors and institution should be acknowledged
% in written form in the publication: “Data processing was carried out
% using the “cSAXS matlab package” developed by the CXS group,
% Paul Scherrer Institut, Switzerland.”
% Variations on the latter text can be incorporated upon discussion with
% the CXS group if needed to more specifically reflect the use of the package
% for the published work.
%
% A publication that focuses on describing features, or parameters, that
% are already existing in the code should be first discussed with the
% authors.
%
% This code and subroutines are part of a continuous development, they
% are provided “as they are” without guarantees or liability on part
% of PSI or the authors. It is the user responsibility to ensure its
% proper use and the correctness of the results.
function [varargout] = spec_read(specDatFile, varargin)
import io.*
import utils.find_files
% check minimum number of input arguments
if(~isunix)
error(['The function ''spec_read'' relies on various system calls,\n' ...
' currently available only on UNIX-like systems\n']);
end
if (nargin<1)
spec_help(mfilename);
error('At least the spec data filename has to be specified as input parameter.')
end
% accept cell array with name/value pairs as well
no_of_in_arg = nargin;
if (nargin == 2)
if (isempty(varargin))
% ignore empty cell array
no_of_in_arg = no_of_in_arg -1;
else
if (iscell(varargin{1}))
% use a filled one given as first and only variable parameter
varargin = varargin{1};
no_of_in_arg = 1 + length(varargin);
end
end
end
% check number of input arguments
if (rem(no_of_in_arg,2) ~= 1)
error('The optional parameters have to be specified as ''name'',''value'' pairs');
end
% here the default parameters
scannr = -1;
output_arg = {'meta','motor','counter'};
unhandled_par_error = 1;
force_cell = 0;
% other parameters
burstn0 = 1;
mexpn0 = 1;
creader = 1;
orchestraPath = [];
specReadOptions = [];
% parse the variable input arguments
vararg = cell(0,0);
for jj = 1:2:length(varargin)
name = varargin{jj};
value = varargin{jj+1};
switch name
case 'ScanNr'
if (~all(value==round(value)) || any(value==0))
error('The value of ''%s'' needs to be a (vector of) integer(s) not equal to zero', name)
end
scannr = value;
case 'Burst'
if (~all(value==round(value)) || any(value<=0))
error('The value of ''%s'' needs to be a positive integer', name)
end
burstn0 = max(1,value);
mexpn0 = 1;
case 'MultExp'
if (~all(value==round(value)) || any(value<=0))
error('The value of ''%s'' needs to be a positive integer', name)
end
burstn0 = 1;
mexpn0 = max(1,value);
case 'OutPut'
output_arg = set_TextFlag(output_arg,value);
case 'PilatusMask'
pilatusMask = value;
output_arg = set_TextFlag(output_arg,'+pilatus');
case 'PilatusDir'
pilatusDir0 = value;
output_arg = set_TextFlag(output_arg,'+pilatus');
case 'Cell'
force_cell = value;
case 'CReader'
creader = value;
case 'Orchestra'
orchestraPath = value;
case 'UnhandledParError'
unhandled_par_error = value;
otherwise
vararg{end+1} = name; %#ok<AGROW>
vararg{end+1} = value; %#ok<AGROW>
end
end
specDatFile = beamline.find_specDatFile(specDatFile);
if creader
try
if ~isempty(orchestraPath)
specReadOptions = [specReadOptions ' --orchestra ' orchestraPath];
end
sysCall = [ fullfile(fileparts(mfilename('fullpath')), './spec_reader/spec_reader') ' -s ' specDatFile ' --scanNr ' strjoin(arrayfun(@(x) num2str(x),scannr,'UniformOutput',false),',') specReadOptions];
[stat, out] = system(sysCall);
if stat
error(['Fast spec reader failed: ' strtrim(out)])
end
res = jsondecode([ out ]);
if length(res)==1
varargout{1} = res;
else
varargout{1} = num2cell(res)';
end
catch ME
if creader
warning('Fast spec reader failed.')
disp(ME)
creader = 0;
end
end
end
if ~creader
% reading the spec file for the scans
if ~exist(specDatFile, 'file')
error('Spec file was not found in %s', specDatFile)
end
[scans,scanline] = spec_readscan(specDatFile, scannr);
% reading the spec file for configuration information
[motorc,motorline] = spec_readconfig(specDatFile);
motorn = cell(size(scannr));
for jj=1:numel(scans)
motorn{jj} = motorc{find(motorline<scanline(1),1,'last')};
end
varargout{1} = cell(size(scans));
% copying vararg in order to keep its content for each iteration
vararg_1 = vararg;
vararg_1{end+1} = 'UnhandledParError';
vararg_1{end+1} = 0;
for jj=1:numel(scans)
scanstr = scans{jj}';
arrout = regexp(scanstr{1},' +','split');
scannr(jj) = str2double(arrout{2});
% get the motors
line = ~cellfun(@isempty,regexp(scanstr,'^#P'));
arrout = reshape(transpose(strvcat((scanstr(line)))),1,[]);
arrout = regexp(arrout,' +|(#P[0-9]+)','split');
motorv = str2double(arrout(~cellfun(@isempty,arrout)));
% get the counters
line = ~cellfun(@isempty,regexp(scanstr,'^#L'));
counters = regexp(scanstr{line},' +','split');
counters = counters(2:end);
% get the data
line = ~cellfun(@isempty,regexp(scanstr,'^[0-9+-]'));
data = cellfun(@str2num,scanstr(line),'UniformOutput',false);
data = cell2mat(data(:));
% get Pilatus information if required
if (exist('pilatusMask','var'))
if (exist('pilatusDir0','var'))
pilatusDir = find_pilatusDir(pilatusDir0,scannr(jj));
else
pilatusDir = '';
end
[pilatusDir, pilatusName, vararg] = ...
find_files(strcat(pilatusDir,pilatusMask), vararg_1);
pilatusInd = zeros(numel(pilatusName),2);
for ii=1:numel(pilatusName)
arrout = regexp(pilatusName(ii).name,'[_\.]','split');
pilatusInd(ii,:) = str2double(arrout(end-2:end-1));
end
end
% make a structure
scan_structure = struct;
if (any(strcmp(output_arg,'motor')) || ...
any(strcmp(output_arg,'motors')))
for ii=1:numel(motorn{jj})
scan_structure.(motorn{jj}{ii}) = motorv(ii);
end
end
if (any(strcmp(output_arg,'meta')))
scan_structure.S = scanstr{1};
% get the time stamp and convert it to a MATLAB-compatible date string
line = ~cellfun(@isempty,regexp(scanstr,'^#D'));
datestr = regexp(scanstr{line},' +','split');
scan_structure.D = sprintf('%s-%s-%s %s', ...
datestr{4}, ...
datestr{3}, ...
datestr{6}, ...
datestr{5});
line = ~cellfun(@isempty,regexp(scanstr,'^#C meta'));
meta = scanstr(line);
for ii=1:length(meta)
metaEntry = strsplit(strtrim(meta{ii}), ' ');
switch metaEntry{4}
case {'int', 'float'}
converterFunc = @str2double;
case 'string'
converterFunc = @(x) x;
end
tmp = [];
for jjj=1:str2double(metaEntry{5})
tmp = [tmp converterFunc(metaEntry{5+jjj})];
end
scan_structure.(metaEntry{3}) = tmp;
end
end
if (any(strcmp(output_arg,'counter')) || ...
any(strcmp(output_arg,'counters')))
if (numel(data)>0)
for ii=1:numel(counters)
scan_structure.(counters{ii}) = data(:,ii);
end
end
end
if (any(strcmp(output_arg,'pilatus')))
if (burstn0>1)
burstn = burstn0;
elseif (isfield(scan_structure,'burstn'))
burstn = max(ones(size(scan_structure.burstn)),scan_structure.burstn);
else
burstn = burstn0;
end
if (mexpn0>1)
mexpn = mexpn0;
elseif (isfield(scan_structure,'mexpn'))
mexpn = max(ones(size(scan_structure.burstn)),scan_structure.mexpn);
else
mexpn = mexpn0;
end
if (numel(burstn)==1 && numel(mexpn)==1)
% these pseudo motors shouldn't be scanned and are
% therefore presumably constant
Pilatus = cell(size(data,1),1);
scanInd = [transpose(floor((0:size(data,1)-1)/mexpn)), ...
transpose(mod(0:size(data,1)-1,mexpn))];
for ii=1:size(data,1)
if (burstn<=1)
indices = all(ones(size(pilatusName))'*scanInd(ii,:)==pilatusInd,2);
else
indices = all(ones(size(pilatusName))'*scanInd(ii,1)==pilatusInd(:,1),2);
end
Pilatus{ii} = {pilatusName(indices).name};
if (numel(indices)<burstn)
% accounting for missing frames
% untested, as of Dec 16
tmp = Pilatus{ii};
Pilatus{ii} = cell(1,burstn);
for kk=1:numel(tmp)
Pilatus{ii}{pilatusInd(2,kk)} = tmp{kk};
end
end
end
end
scan_structure.Pilatus = Pilatus;
scan_structure.PilatusDir = pilatusDir;
end
% append orchestra data
if ~isempty(orchestraPath)
[config, data] = readOrchestraFile(orchestraPath, scannr(jj));
for oidx=1:length(config)
scan_structure.(config{oidx}) = data{oidx};
end
end
varargout{1}{jj} = scan_structure;
end
if ((unhandled_par_error) && (~isempty(vararg)))
vararg %#ok<NOPRT>
error('Not all named parameters have been handled.');
end
if (numel(varargout{1})==1 && ~force_cell)
varargout{1} = varargout{1}{1};
end
varargout{2} = vararg;
return
end
end
%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [varargout] = spec_readscan(specDatFile, scannr)
import io.*
import utils.*
% check minimum number of input arguments
if (nargin<2)
spec_read_help(mfilename);
error('usage ''spec_readscan(specDatFile, scannr)''');
end
cmd = sprintf('grep -n ''#S '' %s', specDatFile);
[~,sysout] = system(cmd);
arrout = regexp(sysout,'[:\n]','split');
arrout = arrout(~cellfun(@isempty,arrout));
arrout = transpose(reshape(arrout,2,[]));
[s1,~] = size(arrout);
if (any(scannr>0))
tmp = regexp(arrout(:,2),' +','split');
scanID = zeros(size(tmp));
for ii=1:numel(tmp)
scanID(ii) = str2double(tmp{ii}{2});
end
end
% creating a look up table where the scans begin and end
lineI = zeros(size(scannr));
scans = cell(size(scannr));
for ii=1:numel(scannr)
if (scannr(ii)<0)
if (-scannr(ii)>size(arrout,1))
error('There does not seem to be sufficiently many scans in ''%s''', ...
specDatFile);
end
tmp = regexp(arrout(end+scannr(ii)+1,:),' +','split');
lineI(ii) = str2double(tmp{1});
if (scannr(ii) < -1)
tmp = regexp(arrout(end+scannr(ii)+2,:),' +','split');
lineF = str2double(tmp{1})-1;
else
cmd = sprintf('wc -l %s', specDatFile);
[~,sysout] = system(cmd);
lineF = str2double(regexp(sysout,'[0-9]+ ','match'));
end
scannr(ii) = str2double(tmp{2}(2));
else
tmp = find((scannr(ii)==scanID),1,'last');
try
verbose(2,'reading ''%s''',arrout{tmp,2});
catch
fprintf('reading ''%s''\n',arrout{tmp,2});
end
if (isempty(tmp))
fprintf('Do not find scan #S %d in ''%s''.\n', ...
scannr(ii),specDatFile);
continue
end
lineI(ii) = str2double(arrout(tmp,1));
if (tmp<s1)
lineF = str2double(arrout(tmp+1,1))-1;
else
cmd = sprintf('wc -l %s', specDatFile);
[~,sysout] = system(cmd);
lineF = str2double(regexp(sysout,'[0-9]+ ','match'));
end
end
cmd = sprintf('head -n +%d %s | tail -n -%d', ...
lineF, specDatFile, lineF+1-lineI(ii));
% read the scan
[~,sysout] = system(cmd);
scans{ii} = regexp(sysout,'\n','split');
scans{ii} = scans{ii}(~cellfun(@isempty,scans{ii}));
end
varargout{1} = scans;
varargout{2} = lineI;
end
%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [motors,linenr] = spec_readconfig(specDatFile)
import io.*
import utils.find_files
% finding the end of the last config
cmd = sprintf('grep -nE ''^#O[0-9]+ '' %s', ...
specDatFile);
[~,sysout] = system(cmd);
arrout = regexp(sysout,'[:\n]','split');
arrout = arrout(~cellfun(@isempty,arrout));
arrout = transpose(reshape(arrout,2,[]));
[s1,~] = size(arrout);
% devide this collection of configuration information into single chuncks
linenr = '';
motors = cell(0);
for ii=1:s1
if (~isempty(regexp(arrout{ii,2},'^#O0+','match')))
if (isempty(linenr))
linenr = str2double(arrout{ii,1});
else
linenr = vertcat(linenr, ...
str2double(arrout{ii,1}));
end
motors{numel(linenr)} = regexp(arrout{ii,2},'(^#O[0-9]+ *)| *','split');
else
motors{numel(linenr)} = horzcat(motors{numel(linenr)}, ...
regexp(arrout{ii,2},'(^#O[0-9]+ *)| *','split'));
end
end
for ii=1:numel(linenr)
motors{ii} = motors{ii}(~cellfun(@isempty,motors{ii}));
end
end
%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function pilatusDir = find_pilatusDir(pilatusDir,scannr)
import io.*
import utils.find_files
while (any(exist(pilatusDir,'dir') == [2,7]))
% if the variable pilatusDir is not a complete path to a file
% try to guess where a spec data file can be found, by
% - look for directories called 'spec' or 'dat-files'
% - look for files called '*.dat'
% - take the newest one
compare_str = pilatusDir;
fname = dir(pilatusDir);
if (exist(pilatusDir,'dir'))
if (pilatusDir(end) ~= '/')
pilatusDir = strcat(pilatusDir,'/');
end
for ii=1:numel(fname)
if (strcmp(fname(ii).name,sprintf('S%02d000-%02d999',floor(scannr/1e3),floor(scannr/1e3))) || ...
strcmp(fname(ii).name,sprintf('S%05d',scannr)))
pilatusDir = strcat(pilatusDir,fname(ii).name);
fname = [];
break;
end
end
for ii=1:numel(fname)
if (strcmp(fname(ii).name,'pilatus'))
pilatusDir = strcat(pilatusDir,fname(ii).name);
break;
end
end
end
if (strcmp(pilatusDir,compare_str))
break
end
end
end
%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [flags] = set_TextFlag(flags,value)
import io.*
import utils.find_files
if (~iscell(value))
value = {value};
end
for ii=1:numel(value)
value_i = value{ii};
if (regexp(value_i,'^[a-zA-Z]+$'))
flags = {value_i};
if (ii+1<=numel(value))
value{ii+1} = regexprep(value{ii+1},'^([a-zA-Z]*)','+$1');
end
elseif (regexp(value_i,'^\+[a-zA-Z]+$'))
flags = unique([flags,value_i(2:end)]);
if (ii+1<=numel(value))
value{ii+1} = regexprep(value{ii+1},'^([a-zA-Z]*)','+$1');
end
elseif (regexp(value_i,'^-[a-zA-Z]+$'))
flags = flags(~strcmp(flags,value_i(2:end)));
if (ii+1<=numel(value))
value{ii+1} = regexprep(value{ii+1},'^([a-zA-Z]*)','-$1');
end
end
end
end
function [config, data] = readOrchestraFile(orchestraPath, scanNr)
config = [];
data = [];
fname = fullfile(orchestraPath, sprintf('scan_%05d.dat', scanNr));
if ~exist(fname, 'file')
warning('Could not find any orchestra file for scan %d', scanNr);
return;
end
fid = fopen(fname);
fgetl(fid);
config = strsplit(fgetl(fid), ' ');
data=textscan(fid,repmat('%f ', 1, length(config)));
end